Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “electrostatics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,423 records · Page 79Linked to original sources
PubMed2005

Effects of lactose permease of Escherichia coli on the anisotropy and electrostatic surface potential of liposomes.

The membrane transport protein lactose permease (LacY), a member of the Major Facilitator Superfamily (MFS) containing twelve membrane-spanning segments connected by hydrophilic loops, was reconstituted in liposomes of: (i) 1,2-dimyristoyl-sn-glycero-3-phosphocoline (DMPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) in equimolar proportions; and (ii) Escherichia coli total lipid extract. The structural order of the lipid membranes, in the presence and absence of LacY, was investigated using steady-state fluorescence anisotropy. The features of the anisotropy curves obtained with 1,6-phenyl-1,3,5-hexatriene (DPH) and 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene p-toluene sulfonate (TMA-DPH) evidenced: (i) the insertion of LacY into the bilayer; and (ii) a surface effect on the membranes. The most dramatic effects were observed when LacY was reconstituted in the E. coli lipid matrix. The effect of the protein on the electrostatic surface potential of each bilayer was also examined using a fluorescent pH indicator, 4-Heptadecyl-7-hydroxycoumarin (HHC). Changes in surface potential were enhanced in the presence of the substrate (i.e. lactose) only when the lipid matrices were charged. These results suggest a role for charged phospholipids (i.e. phosphatidylethanolamine or phosphatidylglycerol) in proton transfer to the amino acids involved in substrate translocation.

Anisotropy↗
PubMed2006

Electrostatic calculations and quantitative protein retention models for ion exchange chromatography.

A novel set of protein descriptors has been developed to increase the understanding of protein behavior on chromatographic media. The protein descriptors are pH-dependent and based on electrostatic and hydrophobic properties of mainly the surface of the proteins as revealed by their three-dimensional structure. Interpretable and predictive quantitative structure property relationship (QSPR) models were then obtained for protein retention in ion exchange chromatography at different pH values. In most cases the calculated average surface potential could be directly related to retention times. Moreover, the high retention of human lactoferrin observed in cation exchange even at high pH values could be modeled by adding descriptors of the charge asymmetry.

Animals↗
PubMed2004

Electrostatic effects on the yield stress of whey protein isolate foams.

The mechanisms responsible for foam structure are of practical interest within the food industry. The yield stress (tau) of whey protein isolate (WPI) foams as affected by electrostatic forces was investigated by whipping 10% (w/v) protein solutions prepared over a range of pH levels and salt concentrations. Measurements of foam overrun and model WPI interfaces, i.e. adsorption kinetics as determined via dynamic surface tension and dilatational rheological characterization, aided data interpretation. Interfacial measurements were also made with the primary whey proteins, beta-lactoglobulin (beta-lg) and alpha-lactalbumin (alpha-la). Yield stress of WPI foams was dependent on pH, salt type and salt concentration. In the absence of salt, tau was highest at pH 5.0 and lowest at pH 3.0. The addition of NaCl and CaCl2 up to 400 mM significantly increased tau at pH 7.0 but not at pH 3.0. Furthermore, at pH 7.0, equivalent molar concentrations of CaCl2 as compared to NaCl increased tau to greater extents. Salts had minimal effects on tau at pH 5.0. Comparisons with interfacial rheological data suggested the protein's capacity to contribute towards tau was related to the protein's potential at forming strong, elastic interfaces throughout the structure. The dynamic surface tension data for beta-lg and alpha-la were similar to WPI, while the interfacial rheological data displayed several noticeable differences.

Adsorption↗
PubMed2005

Electrostatic interactions between model mitochondrial membranes.

Lipids are very diverse in both their respective structures and functions; and cells exquisitely control membrane composition. One intriguing issue is the specific role of lipids in modulating the physical properties of membranes. Cardiolipin (CL) is a unique four-tailed, doubly negatively charged lipid found predominately within the inner mitochondrial membrane, and is thought to be influential in determining the inner mitochondrial membrane potential and permeability. To determine the role of cardiolipin in modulating the charge properties of membranes, this study investigated the electrostatic interactions between mixed cardiolipin and phosphatidylcholine bilayers as a function of cardiolipin concentration. For physiologically relevant concentrations of cardiolipin, the surface charge density of the membrane was found to increase linearly with increasing concentration of cardiolipin. However, only a fraction of the cardiolipin molecules predicted to carry a charge from pK-values were ionized. Clearly environmental factors, beyond that of pH, play a role in determining the charge of bilayers containing cardiolipin.

Adsorption↗
PubMed2005

An elaboration on the syn-anti proton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy.

An in silico survey of all known 3D-structures of glycoside hydrolases that contain a ligand in the -1 subsite is presented. A recurrent crucial positioning of active site residues indicates a common general strategy for electrostatic stabilisation directed to the carbohydrate's ring-oxygen at the transition state. This is substantially different depending on whether the enzyme's proton donor is syn or anti positioned versus the substrate. A comprehensive list of enzymes belonging to 42 different families is given and selected examples are described. An implication for an early evolution scenario of glycoside hydrolases is discussed.

Animals↗
PubMed2005

Electrostatic influence of active-site waters on the nucleophilic aromatic substitution catalyzed by 4-chlorobenzoyl-CoA dehalogenase.

The 4-chlorobenzoyl-CoA dehalogenase catalyzes the hydrolytic dechlorination of 4-chlorobenzoyl-CoA via a two-step mechanism, namely nucleophilic aromatic substitution and ester hydrolysis. The mutation of an active-site Histidine residue has been shown to reduce the catalytic activity in both the substitution and subsequent hydrolysis steps. In this communication, we report a quantum mechanical/molecular mechanical simulation of the potential of mean force for the substitution step, which confirms the increased barrier height in the H90Q mutant and provides evidence on the electrostatic influence of two active-site waters on the rate-limiting barrier.

Amino Acid Substitution↗
PubMed2006

Effects of pH and ionic strength on the assembly and bundling of FtsZ protofilaments: a possible role of electrostatic interactions in the bundling of protofilaments.

Assembly, bundling and stability of FtsZ protofilaments are important for the formation and functioning of the cytokinetic Z-ring during bacterial division. We found that the bundling of FtsZ protofilaments decreased strongly with increasing pH from 6.0 to 7.9, while the assembly of FtsZ monomers did not decrease considerably. In addition, the disassembly of FtsZ protofilaments was strongly suppressed at pH 6.0 as compared to the elevated pHs. The far-UV circular dichroism spectra of the native FtsZ and the tryptophan emission spectra of mutated FtsZ (Y371W) did not change by increasing pH from 6 to 7.9 indicating that the structure of FtsZ was not altered significantly. Further, the inhibition of bundling of FtsZ protofilaments predominantly, and the inhibition of assembly to a lesser extent by salt indicated that electrostatic interactions are important for the assembly and bundling of FtsZ protofilaments. These observations are supported by the results of computational docking of Escherichia coli dimer structure. The results suggest that the basic intracellular pH (7.4-7.8) of E. coli may play a role in regulating the assembly dynamics of FtsZ in the Z-ring by reducing protofilament stability and bundling in bacterial cytoplasm.

Escherichia coli↗
PubMed2005

Improved sensitivity and mass range in time-of-flight bioaerosol mass spectrometry using an electrostatic ion guide.

Bioearosol mass spectrometry (BAMS) analyzes single particles in real time from ambient air, placing strict demands on instrument sensitivity. Modeling of the BAMS reflectron time of flight (TOF) with SIMION revealed design limitations associated with ion transmission and instrument sensitivity at higher masses. Design and implementation of a BAMS linear TOF with electrostatic ion guide and delayed extraction capabilities has greatly increased the sensitivity and mass range relative to the reflectron design. Initial experimental assessment of the new instrument design revealed improved sensitivity at high masses as illustrated when using standard particles of cytochrome C (m/z approximately 12,000), from which the compound's monomer, dimer (m/z approximately 24,000) and trimer (m/z approximately 36,000) were readily detected.

Aerosols↗
PubMed2005

Scalable encapsulation of hepatocytes by electrostatic spraying.

Encapsulating cells by polyelectrolyte complex coacervation can be accomplished at physiological temperature and buffer conditions. One of the oppositely charged polyelectrolytes in the microcapsule core can be collagen or any other natural extra-cellular matrices suitable for cellular support while the other polyelectrolyte forms the ultra-thin shell to ensure efficient mass transfer. These microcapsules with ultra-thin shell are difficult to produce in large quantities due to their fragility. In this study, electrostatic spraying technique was used to achieve a scalable production of one such type of microcapsules formed by complex coacervation between the cationic methylated collagen and anionic terpolymer of hydroxylethyl methacrylate, methyl methacrylate and methylacrylic acid (HEMA-MMA-MAA). It was found that the microcapsule sizes were dependent on several important operational parameters, such as the diameter of the spraying needle, the flow rate of the hepatocytes-collagen mixture and the voltage of the electrical field. The microcapsules with diameters of 200-800 microm and a narrow size distribution (standard deviation of 5-28%) were successfully produced. The above parameters also influenced the hepatocyte viability and functions. With a practical encapsulation rate of up to 55 ml/h per orifice required in bio-artificial liver-assisted device applications, we have produced large quantities of microcapsules maintaining comparable cell viability (>87%), mechanical stability and bio-functions to the manually extruded microcapsules.

Animals↗
PubMed2006

Amperometric immunosensor based on toluidine blue/nano-Au through electrostatic interaction for determination of carcinoembryonic antigen.

A new current amplified immunosensor for the determination of carcinoembryonic antigen (CEA) was demonstrated in this work. The electrode architecture was fabricated by positively charged toluidine blue (TB) coated on negatively charged poly-sulfanilic acid (PSAA) modified glassy carbon electrode (GCE) surface through electrostatic interactions to form a TB/PSAA film, which provided an interface containing amine groups to assemble gold nanoparticles (nano-Au) for immobilization of carcinoembryonic antibody (anti-CEA) and horseradish peroxidase (HRP) instead of bovine serum albumin (BSA) to block sites against non-specific binding. Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) were employed to characterize the electrochemical properties of the modified processes. The CVs reduction current of the immunosensor charged linearly in two concentration ranges of CEA from 0.5 to 5.0 and 5.0 to 120.0 ng/ml in presence of 0.3mM H2O2 in analyte solution, and the detection limit was 0.2 ng/ml at three times background noise. The proposed method is economical, efficient and potentially attractive for clinical immunoassays.

Biosensing Techniques↗
PubMed2004

Electrostatic potentials and fields in the vicinity of engineered nanostructures.

We have developed a method for calculating the electrostatic potentials and fields in the vicinity of geometrically complex engineered nanostructures composed of varying materials in electrolytes of arbitrary pH and ionic strength. The method involves direct summation of charged Debye-Hückel spheres composing the nanostructural surfaces and, by including charge redistribution on the surface of conducting materials held at constant potential, is applicable to mixed boundary conditions. The method is validated by comparison to analytical solutions for an infinite plane (Gouy-Chapman), an infinite cylinder (Bessel functions), and an infinite plane which contains a hole and which is held at constant potential. Excellent agreement between the potentials obtained by our numerical method and the closed form solutions is found for these conditions. The method is applied to the calculation of the electric field enhancement in the vicinity of a nanomembrane whose pore wall is held at constant charge and whose membrane surfaces are held at constant potential. The electric field is found to be enhanced by the charge buildup in the rim of the hole of the nanomembrane; the buildup results from the potential being held constant in the conducting region. Ion concentrations are also calculated. Positive ion rejection is found to be enhanced by this charge buildup in the region of the rim when a constant positive potential is applied.

Journal Article↗
PubMed2006

Nanoscale electrostatic actuators in liquid electrolytes.

Equilibrium and energy analyses were performed for an electrostatic actuator consisting of two plane parallel electrodes, operated using DC voltages, separated by a liquid electrolyte. One electrode is fixed, and the other electrode is connected to a spring and is free to move. The mechanical equilibrium includes the spring force, the van der Waals force, and the electrochemical force as given by the solution of the linearized Poisson-Boltzmann equation. The electrode separation is determined as a function of the applied potential, the natural (i.e., zeta) potential, the Debeye length, the initial electrode separation, the spring constant, and the Hamaker constant. The actuator exhibits the classical "pull-in" instability. The natural potential increases the critical applied potential but does not significantly affect the critical separation. For zero natural potential, the spring constant does not affect the critical separation. Ratios of the maximum spring energy, the maximum van der Waals energy, and the maximum electrochemical energy were plotted as functions of the Hamaker constant and the initial electrode separation.

Journal Article↗
PubMed2005

Drosophila alcohol dehydrogenase: acetate-enzyme interactions and novel insights into the effects of electrostatics on catalysis.

Drosophila alcohol dehydrogenase (DADH) is an NAD+-dependent enzyme that catalyzes the oxidation of alcohols to aldehydes/ketones and that is also able to further oxidize aldehydes to their corresponding carboxylic acids. The structure of the ternary enzyme-NADH-acetate complex of the slow alleloform of Drosophila melanogaster ADH (DmADH-S) was solved at 1.6 A resolution by X-ray crystallography. The coenzyme stereochemistry of the aldehyde dismutation reaction showed that the obtained enzyme-NADH-acetate complex reflects a productive ternary complex although no enzymatic reaction occurs. The stereochemistry of the acetate binding in the bifurcated substrate-binding site, along with previous stereochemical studies of aldehyde reduction and alcohol oxidation shows that the methyl group of the aldehyde in the reduction reaction binds to the R1 and in the oxidation reaction to the R2 sub-site. NMR studies along with previous kinetic studies show that the formed acetaldehyde intermediate in the oxidation of ethanol to acetate leaves the substrate site prior to the reduced coenzyme, and then binds to the newly formed enzyme-NAD+ complex. Here, we compare the three-dimensional structure of D.melanogaster ADH-S and a previous theoretically built model, evaluate the differences with the crystal structures of five Drosophila lebanonensis ADHs in numerous complexed forms that explain the substrate specificity as well as subtle kinetic differences between these two enzymes based on their crystal structures. We also re-examine the electrostatic influence of charged residues on the surface of the protein on the catalytic efficiency of the enzyme.

Acetates↗
PubMed2004

Molecular modeling of sigma 1 receptor ligands: a model of binding conformational and electrostatic considerations.

We have performed molecular modeling studies on several sigma 1 specific ligands, including PD144418, spipethiane, haloperidol, pentazocine, and others to develop a pharmacophore for sigma 1 receptor-ligand binding, under the assumption that all the compounds interact at the same receptor binding site. The modeling studies have investigated the conformational and electrostatic properties of the ligands. Superposition of active molecules gave the coordinates of the hypothetical 5-point sigma 1 pharmacophore, as follows: R1 (0.85, 7.26, 0.30); R2 (5.47, 2.40, -1.51); R3 (-2.57, 4.82, -7.10); N (-0.71, 3.29, -6.40); carbon centroid (3.16, 4.83, -0.60), where R1, R2 were constructed onto the aromatic ring of each compound to represent hydrophobic interactions with the receptor; and R3 represents a hydrogen bond between the nitrogen atom and the receptor. Additional analyses were used to describe secondary binding sites to electronegative groups such as oxygen or sulfur atom. Those coordinates are (2.34, 5.08, -4.18). The model was verified by fitting other sigma 1 receptor ligands. This model may be used to search conformational databases for other possibly active ligands. In conjunction with rational drug design techniques the model may be useful in design and synthesis of novel sigma 1 ligands of high selectivity and potency. Calculations were performed using Sybyl 6.5.

Binding Sites↗
PubMed2005

A model for the interaction between plant GAPN and 14-3-3zeta using protein-protein docking calculations, electrostatic potentials and kinetics.

Phosphorylated non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9; GAPN) found in heterotrophic cells of wheat is activated by MgCl(2). The divalent cation disrupts the interaction between GAPN and a 14-3-3 regulatory protein. This effect is quite remarkable, since it has previously been shown that 14-3-3 binding to a target protein requires divalent cations as Mg(2+) or Ca(2+). Binding of the divalent cation to 14-3-3 causes an increase in surface hydrophobicity. Crystal structure of a 14-3-3-target protein complex has been only determined for serotinin N-acetyltransferase. We utilized a model of a subunit of plant GAPN and the crystallographic structure of human 14-3-3zeta to shape the complex between theses two proteins. Initial dockings were performed with the BiGGER program, which allows an exhaustive search of translational and rotational space. A filtering procedure was then applied to reduce the number of complexes to a manageable number. We predict the structural characteristics of GAPN-14-3-3zeta binding process, proposing that the main attractive force in this complex derives from electrostatic interactions. The predicted model was corroborated by analysis of kinetic behavior of GAPN and its relationship with pH and ionic strength conditions. This study provides a variant on the interaction of 14-3-3 with target proteins, thus affording a wider scenario to establish possible structural models for this remarkable family of regulatory proteins.

14-3-3 Proteins↗
PubMed2006

Current-source density estimation based on inversion of electrostatic forward solution: effects of finite extent of neuronal activity and conductivity discontinuities.

A new method for estimation of current-source density (CSD) from local field potentials is presented. This inverse CSD (iCSD) method is based on explicit inversion of the electrostatic forward solution and can be applied to data from multielectrode arrays with various geometries. Here, the method is applied to linear-array (laminar) electrode data. Three iCSD methods are considered: the CSD is assumed to have cylindrical symmetry and be (i) localized in infinitely thin discs, (ii) step-wise constant or (iii) continuous and smoothly varying (using cubic splines) in the vertical direction. For spatially confined CSD distributions the standard CSD method, involving a discrete double derivative, is seen in model calculations to give significant estimation errors when the lateral source dimension is comparable to the size of a cortical column (less than approximately 1 mm). Further, discontinuities in the extracellular conductivity are seen to potentially give sizable errors for even wider source distributions. The iCSD methods are seen to give excellent estimates when the correct lateral source dimension and spatial distribution of conductivity are incorporated. To illustrate the application to real data, iCSD estimates of stimulus-evoked responses measured with laminar electrodes in the rat somatosensory (barrel) cortex are compared to estimates from the standard CSD method.

Algorithms↗
PubMed2003

Effect of channel geometry on the electrostatic potential in acetylcholine channels.

We study the effect of channel geometry on the potential barrier encountered by ions as they permeate the acetylcholine receptor channel. Among the various channel geometries which have been used to represent the acetylcholine receptor channel include the cylinder and the toroidal catenary. The main reasons for those choices appear to be the facilitation of separation of the Poisson equation, rather than biological considerations. We consider a novel and realistic acetylcholine channel geometry, and calculate the electrostatic potential profiles within it, and compare our results with results from other channel geometries.

Membrane Potentials↗
PubMed2005

A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada.

The transcriptional activity of many sequence-specific DNA binding proteins is directly regulated by posttranslational covalent modification. Although this form of regulation was first described nearly two decades ago, it remains poorly understood at a mechanistic level. The prototype for a transcription factor controlled by posttranslational modification is E. coli Ada protein, a chemosensor that both repairs methylation damage in DNA and coordinates the resistance response to genotoxic methylating agents. Ada repairs methyl phosphotriester lesions in DNA by transferring the aberrant methyl group to one of its own cysteine residues; this site-specific methylation enhances tremendously the DNA binding activity of the protein, thereby enabling it to activate a methylation-resistance regulon. Here, we report solution and X-ray structures of the Cys-methylated chemosensor domain of Ada bound to DNA. The structures reveal that both phosphotriester repair and methylation-dependent transcriptional activation function through a zinc- and methylation-dependent electrostatic switch.

Crystallography, X-Ray↗